filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 /**************************************************************************************/
  14
  15 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18                 filterFileName = "";
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         map<string,string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51
  52                                 it = parameters.find("hard");
  53                                 //user has given a template file
  54                                 if(it != parameters.end()){
  55                                         path = hasPath(it->second);
  56                                         //if the user has not given a path then, add inputdir. else leave path alone.
  57                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
  58                                 }
  59                         }
  60
  61                         //check for required parameters
  62                         fasta = validParameter.validFile(parameters, "fasta", false);
  63                         if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
  64                         else {
  65                                 splitAtDash(fasta, fastafileNames);
  66
  67                                 //go through files and make sure they are good, if not, then disregard them
  68                                 for (int i = 0; i < fastafileNames.size(); i++) {
  69                                         if (inputDir != "") {
  70                                                 string path = hasPath(fastafileNames[i]);
  71                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  72                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
  73                                         }
  74
  75                                         int ableToOpen;
  76                                         ifstream in;
  77                                         ableToOpen = openInputFile(fastafileNames[i], in);
  78                                         if (ableToOpen == 1) {
  79                                                 m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  80                                                 //erase from file list
  81                                                 fastafileNames.erase(fastafileNames.begin()+i);
  82                                                 i--;
  83                                         }else{
  84                                                 string simpleName = getSimpleName(fastafileNames[i]);
  85                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  86                                         }
  87                                         in.close();
  88                                 }
  89
  90                                 //make sure there is at least one valid file left
  91                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  92                         }
  93
  94                         if (!abort) {
  95                                 //if the user changes the output directory command factory will send this info to us in the output parameter
  96                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  97                                         outputDir = "";
  98                                         outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
  99                                 }
 100                         }
 101                         //check for optional parameter and set defaults
 102                         // ...at some point should added some additional type checking...
 103
 104                         string temp;
 105                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 106                         else if (hard == "not open") { hard = ""; abort = true; }
 107
 108                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 109                         trump = temp[0];
 110
 111                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 112                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 113
 114                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 115                         convert(temp, processors);
 116
 117                         vertical = validParameter.validFile(parameters, "vertical", false);
 118                         if (vertical == "not found") {
 119                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 120                                 else { vertical = "F";  }
 121                         }
 122
 123                         numSeqs = 0;
 124                 }
 125
 126         }
 127         catch(exception& e) {
 128                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 129                 exit(1);
 130         }
 131 }
 132
 133 //**********************************************************************************************************************
 134
 135 void FilterSeqsCommand::help(){
 136         try {
 137
 138                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 139                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 140                 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
 141                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 142                 m->mothurOut("The trump parameter .... The default is ...\n");
 143                 m->mothurOut("The soft parameter .... The default is ....\n");
 144                 m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
 145                 m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
 146                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 147                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
 148                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
 149                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 150
 151         }
 152         catch(exception& e) {
 153                 m->errorOut(e, "FilterSeqsCommand", "help");
 154                 exit(1);
 155         }
 156 }
 157
 158 /**************************************************************************************/
 159
 160 int FilterSeqsCommand::execute() {
 161         try {
 162
 163                 if (abort == true) { return 0; }
 164
 165                 ifstream inFASTA;
 166                 openInputFile(fastafileNames[0], inFASTA);
 167
 168                 Sequence testSeq(inFASTA);
 169                 alignmentLength = testSeq.getAlignLength();
 170                 inFASTA.close();
 171
 172                 ////////////create filter/////////////////
 173                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 174
 175                 filter = createFilter();
 176
 177                 m->mothurOutEndLine();  m->mothurOutEndLine();
 178
 179                 if (m->control_pressed) { return 0; }
 180
 181                 #ifdef USE_MPI
 182                         int pid;
 183                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 184
 185                         if (pid == 0) { //only one process should output the filter
 186                 #endif
 187
 188                 ofstream outFilter;
 189
 190                 string filterFile = outputDir + filterFileName + ".filter";
 191                 openOutputFile(filterFile, outFilter);
 192                 outFilter << filter << endl;
 193                 outFilter.close();
 194                 outputNames.push_back(filterFile);
 195
 196                 #ifdef USE_MPI
 197                         }
 198                 #endif
 199
 200                 ////////////run filter/////////////////
 201
 202                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 203
 204                 filterSequences();
 205
 206                 m->mothurOutEndLine();  m->mothurOutEndLine();
 207
 208                 int filteredLength = 0;
 209                 for(int i=0;i<alignmentLength;i++){
 210                         if(filter[i] == '1'){   filteredLength++;       }
 211                 }
 212
 213                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 214
 215
 216                 m->mothurOutEndLine();
 217                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 218                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 219                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 220                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 221
 222
 223                 m->mothurOutEndLine();
 224                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 225                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 226                 m->mothurOutEndLine();
 227
 228                 return 0;
 229
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "FilterSeqsCommand", "execute");
 233                 exit(1);
 234         }
 235 }
 236 /**************************************************************************************/
 237 int FilterSeqsCommand::filterSequences() {
 238         try {
 239
 240                 numSeqs = 0;
 241
 242                 for (int s = 0; s < fastafileNames.size(); s++) {
 243
 244                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 245
 246                                 string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
 247 #ifdef USE_MPI
 248                                 int pid, start, end, numSeqsPerProcessor, num;
 249                                 int tag = 2001;
 250                                 vector<long>MPIPos;
 251
 252                                 MPI_Status status;
 253                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 254                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 255
 256                                 MPI_File outMPI;
 257                                 MPI_File tempMPI;
 258                                 MPI_File inMPI;
 259                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 260                                 int inMode=MPI_MODE_RDONLY;
 261
 262                                 char outFilename[1024];
 263                                 strcpy(outFilename, filteredFasta.c_str());
 264
 265                                 char inFileName[1024];
 266                                 strcpy(inFileName, fastafileNames[s].c_str());
 267
 268                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 269                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 270
 271                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 272
 273                                 if (pid == 0) { //you are the root process
 274
 275                                         MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 276                                         numSeqs += num;
 277
 278                                         //send file positions to all processes
 279                                         for(int i = 1; i < processors; i++) {
 280                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 281                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 282                                         }
 283
 284                                         //figure out how many sequences you have to do
 285                                         numSeqsPerProcessor = num / processors;
 286                                         int startIndex =  pid * numSeqsPerProcessor;
 287                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 288
 289
 290                                         //do your part
 291                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 292
 293                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 294
 295                                         //wait on chidren
 296                                         for(int i = 1; i < processors; i++) {
 297                                                 char buf[4];
 298                                                 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 299                                         }
 300
 301                                 }else { //you are a child process
 302                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 303                                         MPIPos.resize(num+1);
 304                                         numSeqs += num;
 305                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 306
 307                                         //figure out how many sequences you have to align
 308                                         numSeqsPerProcessor = num / processors;
 309                                         int startIndex =  pid * numSeqsPerProcessor;
 310                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 311
 312
 313                                         //align your part
 314                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 315
 316                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 317
 318                                         char buf[4];
 319                                         strcpy(buf, "done");
 320
 321                                         //tell parent you are done.
 322                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 323                                 }
 324
 325                                 MPI_File_close(&outMPI);
 326                                 MPI_File_close(&inMPI);
 327                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 328
 329 #else
 330                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 331                                 if(processors == 1){
 332                                         ifstream inFASTA;
 333                                         int numFastaSeqs;
 334                                         openInputFile(fastafileNames[s], inFASTA);
 335                                         getNumSeqs(inFASTA, numFastaSeqs);
 336                                         inFASTA.close();
 337
 338                                         lines.push_back(new linePair(0, numFastaSeqs));
 339
 340                                         numSeqs += numFastaSeqs;
 341
 342                                         driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 343                                 }else{
 344                                         setLines(fastafileNames[s]);
 345                                         createProcessesRunFilter(filter, fastafileNames[s]);
 346
 347                                         rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
 348
 349                                         //append fasta files
 350                                         for(int i=1;i<processors;i++){
 351                                                 appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
 352                                                 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
 353                                         }
 354                                 }
 355
 356                                 if (m->control_pressed) {  return 1; }
 357                 #else
 358                                 ifstream inFASTA;
 359                                 int numFastaSeqs;
 360                                 openInputFile(fastafileNames[s], inFASTA);
 361                                 getNumSeqs(inFASTA, numFastaSeqs);
 362                                 inFASTA.close();
 363
 364                                 lines.push_back(new linePair(0, numFastaSeqs));
 365
 366                                 numSeqs += numFastaSeqs;
 367
 368                                 driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 369
 370                                 if (m->control_pressed) {  return 1; }
 371                 #endif
 372 #endif
 373                         outputNames.push_back(filteredFasta);
 374                 }
 375
 376                 return 0;
 377         }
 378         catch(exception& e) {
 379                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 380                 exit(1);
 381         }
 382 }
 383 #ifdef USE_MPI
 384 /**************************************************************************************/
 385 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
 386         try {
 387                 string outputString = "";
 388                 int count = 0;
 389                 MPI_Status status;
 390
 391                 for(int i=0;i<num;i++){
 392
 393                         if (m->control_pressed) { return 0; }
 394
 395                         //read next sequence
 396                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 397                         char* buf4 = new char[length];
 398                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 399
 400                         string tempBuf = buf4;
 401                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 402                         istringstream iss (tempBuf,istringstream::in);
 403                         delete buf4;
 404
 405                         Sequence seq(iss);  gobble(iss);
 406
 407                         if (seq.getName() != "") {
 408                                 string align = seq.getAligned();
 409                                 string filterSeq = "";
 410
 411                                 for(int j=0;j<alignmentLength;j++){
 412                                         if(filter[j] == '1'){
 413                                                 filterSeq += align[j];
 414                                         }
 415                                 }
 416
 417                                 count++;
 418                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 419
 420                                 if(count % 10 == 0){ //output to file
 421                                         //send results to parent
 422                                         int length = outputString.length();
 423                                         char* buf = new char[length];
 424                                         memcpy(buf, outputString.c_str(), length);
 425
 426                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 427                                         outputString = "";
 428                                         delete buf;
 429                                 }
 430
 431                         }
 432
 433                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 434                 }
 435
 436                 if(outputString != ""){ //output to file
 437                         //send results to parent
 438                         int length = outputString.length();
 439                         char* buf = new char[length];
 440                         memcpy(buf, outputString.c_str(), length);
 441
 442                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 443                         outputString = "";
 444                         delete buf;
 445                 }
 446
 447                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 448
 449                 return 0;
 450         }
 451         catch(exception& e) {
 452                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 453                 exit(1);
 454         }
 455 }
 456 #endif
 457 /**************************************************************************************/
 458 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
 459         try {
 460                 ofstream out;
 461                 openOutputFile(outputFilename, out);
 462
 463                 ifstream in;
 464                 openInputFile(inputFilename, in);
 465
 466                 in.seekg(line->start);
 467
 468                 for(int i=0;i<line->num;i++){
 469
 470                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 471
 472                                 Sequence seq(in);
 473                                 if (seq.getName() != "") {
 474                                         string align = seq.getAligned();
 475                                         string filterSeq = "";
 476
 477                                         for(int j=0;j<alignmentLength;j++){
 478                                                 if(filter[j] == '1'){
 479                                                         filterSeq += align[j];
 480                                                 }
 481                                         }
 482
 483                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 484                                 }
 485                                 gobble(in);
 486                 }
 487                 out.close();
 488                 in.close();
 489
 490                 return 0;
 491         }
 492         catch(exception& e) {
 493                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 494                 exit(1);
 495         }
 496 }
 497 /**************************************************************************************************/
 498
 499 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 500         try {
 501 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 502                 int process = 0;
 503                 int exitCommand = 1;
 504                 processIDS.clear();
 505
 506                 //loop through and create all the processes you want
 507                 while (process != processors) {
 508                         int pid = fork();
 509
 510                         if (pid > 0) {
 511                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 512                                 process++;
 513                         }else if (pid == 0){
 514                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 515                                 driverRunFilter(F, filteredFasta, filename, lines[process]);
 516                                 exit(0);
 517                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 518                 }
 519
 520                 //force parent to wait until all the processes are done
 521                 for (int i=0;i<processors;i++) {
 522                         int temp = processIDS[i];
 523                         wait(&temp);
 524                 }
 525
 526                 return exitCommand;
 527 #endif
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 531                 exit(1);
 532         }
 533 }
 534 /**************************************************************************************/
 535 string FilterSeqsCommand::createFilter() {
 536         try {
 537                 string filterString = "";
 538                 Filters F;
 539
 540                 if (soft != 0)                  {  F.setSoft(soft);             }
 541                 if (trump != '*')               {  F.setTrump(trump);   }
 542
 543                 F.setLength(alignmentLength);
 544
 545                 if(trump != '*' || isTrue(vertical) || soft != 0){
 546                         F.initialize();
 547                 }
 548
 549                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 550                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 551
 552                 numSeqs = 0;
 553                 if(trump != '*' || isTrue(vertical) || soft != 0){
 554                         for (int s = 0; s < fastafileNames.size(); s++) {
 555
 556                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 557
 558 #ifdef USE_MPI
 559                                 int pid, numSeqsPerProcessor, num;
 560                                 int tag = 2001;
 561                                 vector<long> MPIPos;
 562
 563                                 MPI_Status status;
 564                                 MPI_File inMPI;
 565                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 566                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 567
 568                                 //char* tempFileName = new char(fastafileNames[s].length());
 569                                 //tempFileName = &(fastafileNames[s][0]);
 570
 571                                 char tempFileName[1024];
 572                                 strcpy(tempFileName, fastafileNames[s].c_str());
 573
 574                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 575
 576                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 577
 578                                 if (pid == 0) { //you are the root process
 579                                                 MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 580                                                 numSeqs += num;
 581
 582                                                 //send file positions to all processes
 583                                                 for(int i = 1; i < processors; i++) {
 584                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 585                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 586                                                 }
 587
 588                                                 //figure out how many sequences you have to do
 589                                                 numSeqsPerProcessor = num / processors;
 590                                                 int startIndex =  pid * numSeqsPerProcessor;
 591                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 592
 593
 594                                                 //do your part
 595                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 596
 597                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 598
 599                                 }else { //i am the child process
 600                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 601                                         MPIPos.resize(num+1);
 602                                         numSeqs += num;
 603                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 604
 605                                         //figure out how many sequences you have to align
 606                                         numSeqsPerProcessor = num / processors;
 607                                         int startIndex =  pid * numSeqsPerProcessor;
 608                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 609
 610
 611                                         //do your part
 612                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 613
 614                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 615                                 }
 616
 617                                 MPI_File_close(&inMPI);
 618                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 619
 620 #else
 621                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 622                                 if(processors == 1){
 623                                         ifstream inFASTA;
 624                                         int numFastaSeqs;
 625                                         openInputFile(fastafileNames[s], inFASTA);
 626                                         getNumSeqs(inFASTA, numFastaSeqs);
 627                                         inFASTA.close();
 628
 629                                         numSeqs += numFastaSeqs;
 630
 631                                         lines.push_back(new linePair(0, numFastaSeqs));
 632
 633                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 634                                 }else{
 635                                         setLines(fastafileNames[s]);
 636                                         createProcessesCreateFilter(F, fastafileNames[s]);
 637                                 }
 638
 639                                 if (m->control_pressed) {  return filterString; }
 640                 #else
 641                                 ifstream inFASTA;
 642                                 int numFastaSeqs;
 643                                 openInputFile(fastafileNames[s], inFASTA);
 644                                 getNumSeqs(inFASTA, numFastaSeqs);
 645                                 inFASTA.close();
 646
 647                                 numSeqs += numFastaSeqs;
 648
 649                                 lines.push_back(new linePair(0, numFastaSeqs));
 650
 651                                 driverCreateFilter(F, fastafileNames[s], lines[0]);
 652                                 if (m->control_pressed) {  return filterString; }
 653                 #endif
 654 #endif
 655
 656                         }
 657                 }
 658
 659
 660 #ifdef USE_MPI
 661                 int pid;
 662                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 663                 MPI_Status status;
 664
 665                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 666
 667                 if(trump != '*' || isTrue(vertical) || soft != 0){
 668
 669                         if (pid == 0) { //only one process should output the filter
 670
 671                                 vector<int> temp; temp.resize(alignmentLength+1);
 672
 673                                 //get the frequencies from the child processes
 674                                 for(int i = 1; i < processors; i++) {
 675
 676                                         for (int j = 0; j < 5; j++) {
 677
 678                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 679                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 680
 681                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 682                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 683                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 684                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 685                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 686                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 687                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 688                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 689                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 690                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 691                                                 }
 692                                         }
 693                                 }
 694                         }else{
 695
 696                                 //send my fequency counts
 697                                 F.a.push_back(Atag);
 698                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 699                                 F.t.push_back(Ttag);
 700                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 701                                 F.c.push_back(Ctag);
 702                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 703                                 F.g.push_back(Gtag);
 704                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 705                                 F.gap.push_back(Gaptag);
 706                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 707                         }
 708
 709                 }
 710
 711                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 712
 713                 if (pid == 0) { //only one process should output the filter
 714 #endif
 715                 F.setNumSeqs(numSeqs);
 716
 717                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 718                 if(soft != 0)                           {       F.doSoft();             }
 719
 720                 filterString = F.getFilter();
 721
 722 #ifdef USE_MPI
 723                 //send filter string to kids
 724                 //for(int i = 1; i < processors; i++) {
 725                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 726                 //}
 727                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 728         }else{
 729                 //recieve filterString
 730                 char* tempBuf = new char[alignmentLength];
 731                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 732                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 733
 734                 filterString = tempBuf;
 735                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 736                 delete tempBuf;
 737         }
 738
 739         MPI_Barrier(MPI_COMM_WORLD);
 740 #endif
 741
 742                 return filterString;
 743         }
 744         catch(exception& e) {
 745                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 746                 exit(1);
 747         }
 748 }
 749 /**************************************************************************************/
 750 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 751         try {
 752
 753                 ifstream in;
 754                 openInputFile(filename, in);
 755
 756                 in.seekg(line->start);
 757
 758                 for(int i=0;i<line->num;i++){
 759
 760                         if (m->control_pressed) { in.close(); return 1; }
 761
 762                         Sequence seq(in);
 763                         if (seq.getName() != "") {
 764                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 765
 766                                         if(trump != '*'){       F.doTrump(seq); }
 767                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 768                                         cout.flush();
 769                         }
 770
 771                         //report progress
 772                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 773                 }
 774
 775                 //report progress
 776                 if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
 777
 778                 in.close();
 779
 780                 return 0;
 781         }
 782         catch(exception& e) {
 783                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 784                 exit(1);
 785         }
 786 }
 787 #ifdef USE_MPI
 788 /**************************************************************************************/
 789 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {
 790         try {
 791
 792                 MPI_Status status;
 793                 int pid;
 794                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 795
 796                 for(int i=0;i<num;i++){
 797
 798                         if (m->control_pressed) { return 0; }
 799
 800                         //read next sequence
 801                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 802
 803                         char* buf4 = new char[length];
 804                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 805
 806                         string tempBuf = buf4;
 807                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 808                         istringstream iss (tempBuf,istringstream::in);
 809                         delete buf4;
 810
 811                         Sequence seq(iss);
 812
 813                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
 814
 815                         if(trump != '*'){       F.doTrump(seq); }
 816                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 817                         cout.flush();
 818
 819                         //report progress
 820                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 821                 }
 822
 823                 //report progress
 824                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
 825
 826                 return 0;
 827         }
 828         catch(exception& e) {
 829                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 830                 exit(1);
 831         }
 832 }
 833 #endif
 834 /**************************************************************************************************/
 835
 836 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 837         try {
 838 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 839                 int process = 0;
 840                 int exitCommand = 1;
 841                 processIDS.clear();
 842
 843                 //loop through and create all the processes you want
 844                 while (process != processors) {
 845                         int pid = vfork();
 846
 847                         if (pid > 0) {
 848                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 849                                 process++;
 850                         }else if (pid == 0){
 851                                 driverCreateFilter(F, filename, lines[process]);
 852                                 exit(0);
 853                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 854                 }
 855
 856                 //force parent to wait until all the processes are done
 857                 for (int i=0;i<processors;i++) {
 858                         int temp = processIDS[i];
 859                         wait(&temp);
 860                 }
 861
 862                 return exitCommand;
 863 #endif
 864         }
 865         catch(exception& e) {
 866                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 867                 exit(1);
 868         }
 869 }
 870 /**************************************************************************************************/
 871
 872 int FilterSeqsCommand::setLines(string filename) {
 873         try {
 874
 875                 vector<long int> positions;
 876                 bufferSizes.clear();
 877
 878                 ifstream inFASTA;
 879                 openInputFile(filename, inFASTA);
 880
 881                 string input;
 882                 while(!inFASTA.eof()){
 883                         input = getline(inFASTA);
 884
 885                         if (input.length() != 0) {
 886                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 887                         }
 888                 }
 889                 inFASTA.close();
 890
 891                 int numFastaSeqs = positions.size();
 892
 893                 FILE * pFile;
 894                 long size;
 895
 896                 //get num bytes in file
 897                 pFile = fopen (filename.c_str(),"rb");
 898                 if (pFile==NULL) perror ("Error opening file");
 899                 else{
 900                         fseek (pFile, 0, SEEK_END);
 901                         size=ftell (pFile);
 902                         fclose (pFile);
 903                 }
 904
 905                 numSeqs += numFastaSeqs;
 906
 907                 int numSeqsPerProcessor = numFastaSeqs / processors;
 908
 909                 for (int i = 0; i < processors; i++) {
 910
 911                         long int startPos = positions[ i * numSeqsPerProcessor ];
 912                         if(i == processors - 1){
 913                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 914                                 bufferSizes.push_back(size - startPos);
 915                         }else{
 916                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 917                                 bufferSizes.push_back(myEnd-startPos);
 918                         }
 919                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 920                 }
 921
 922                 return 0;
 923         }
 924         catch(exception& e) {
 925                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 926                 exit(1);
 927         }
 928 }
 929 /**************************************************************************************/